Interpreting the fragmentation pattern of the mass spectrum of hexane

[M]⁺ is the molecular ion peak (M) with an m/z of 86 corresponding to [C₆H₁₄]⁺, the original hexane molecule minus an electron, [CH₃CH₂CH₂CH₂CH₂CH₃]⁺.

The small M+1 peak at m/z 87, corresponds to an ionised hexane molecule with one ¹³C atom in it i.e. an ionised hexane molecule of formula ¹³C¹²C₅H₁₄

Carbon-13 only accounts for ~1% of all carbon atoms (¹²C ~99%), but the more carbon atoms in the molecule, the greater the probability of observing this ¹³C M+1 peak.

Hexane has 6 carbon atoms, so on average, ~1 in 17 molecules of will contain a ¹³C atom.

A similar argument applies to fragment ions from the breakdown of the parent molecular ion of hexane - though the ratio will be greater e.g. the m/z 58 ion.

Identifying the species giving the most prominent peaks (apart from M) in the fragmentation pattern of hexane.

The most abundant ion of the molecule under mass spectrometry investigation is usually given an arbitrary abundance value of 100, called the base ion peak, and all other abundances ('intensities') are measured against it.

Analysing and explaining the principal ions in the fragmentation pattern of the mass spectrum of hexane

Atomic masses: H = 1;  C = 12 (13 for ~1 in 100)

Bond enthalpies = kJ/mol: C-C = 348;  C-H = 412

Examples of possible equations to explain some of the most abundant ion peaks in the mass spectrum of 2-methylpentane

Formation of m/z 71 ion:

[CH₃CH₂CH₂CH₂CH₂CH₃]⁺  ===>  [CH₃CH₂CH₂CH₂CH₂]⁺  +  CH₃

C-C bond scission in the carbon chain of the molecular ion of hexane giving a [C₅H₁₁]⁺ ion.

Mass change: 86 - 15 = 71.

Formation of m/z 57 ion:

[CH₃CH₂CH₂CH₂CH₂CH₃]⁺  ===>  [CH₃CH₂CH₂CH₂]⁺  +  CH₂CH₃

The m/z 57 ion is the base peak ion, the most abundant and 'stable' ion fragment.

Again, C-C bond scission in the carbon chain of the molecular ion of hexane.

Loss of ethyl group, mass change = 86 - 29 = 57.

Similarly the m/z 57 ion could be formed by further scission of a shorter fragment ion.

e.g.: [CH₃CH₂CH₂CH₂CH₂]⁺  ===>  [CH₃CH₂CH₂CH₂]⁺  +  CH₂

Formation of m/z 43 ion:

[CH₃CH₂CH₂CH₂CH₂CH₃]⁺  ===>  [CH₃CH₂CH₂]⁺  +  CH₂CH₂CH₃

C-C bond scission of the parent molecular ion, loss of propyl group, mass change = 86 - 43 = 43.

Formation of m/z 29 ion:

[CH₃CH₂CH₂CH₂CH₂CH₃]⁺  ===>  [CH₃CH₂]⁺  +  CH₂CH₂CH₂CH₃

C-C bond scission of the parent molecular ion, loss of butyl group, mass change = 86 - 57 = 29.

Sequences including m/z values of 42, 41, 40, 39 or 28, 28, 27, 26, indicate successive hydrogen atom/molecule loss from the m/z 43 or 29 ions.

Comparing the infrared, mass, 1H NMR and 13C NMR spectra of the five structural alkane isomers of C6H14 NOTE: The images are linked to their original detailed spectral analysis pages AND can be doubled in size with touch screens to increase the definition to the original hexane, 2-methylpentane, 3-methylpentane, 2,2-dimethylbutane and 2,3-dimethylbutane image sizes.  These five molecules are structural isomers of saturated alkanes of molecular formula C6H14 and exemplify the infrared, mass, 1H NMR and 13C NMR spectra of lower aliphatic alkanes (non-cyclic alkanes).
Infrared spectra below.
	INFRARED SPECTRA: Apart from the significant differences in the fingerprint region at wavenumbers 1500 to 400 cm-1, there are no other great striking differences, but each could be identified from its infrared spectrum. All the absorption bands are typical of molecules containing saturated alkyl structure and there are no characteristic infrared absorptions due to a specific functional group.
Infrared spectra above, mass spectra below.
	MASS SPECTRA: Base ion peaks plus m/z comments. Hexane: m/z 57, 42 and 56 prominent 2-methylpentane: m/z 43, 42 and 71 prominent 3-methylpentane: m/z 57, 41 and 56 prominent 2,2-dimethylbutane: m/z 43, 41, 57 and 71 prominent 2,3-dimethylbutane: m/z 43, 41, 42 and 71 prominent
Mass spectra above, 1H NMR spectra below.
	1H NMR SPECTRA: They can all be distinguished by their different integrated proton ratios - need very high resolution. Hexane: 3 1H δ shifts, H ratio 3:2:2 (6:4:4 in formula) 2-methylpentane: 5 1H δ shifts, H ratio 6:3:2:2:1 3-methylpentane: 4 1H δ shifts, H ratio 6:4:3:1 2,2-dimethylbutane: 3 1H δ shifts, H ratio 9:3:2 2,3-dimethylbutane: 2 1H δ shifts, H ratio 6:1 (12:2 in formula)
1H NMR spectra above, 13C NMR spectra below.
	13C NMR SPECTRA: From the number of shifts, you can't distinguish (iii) and (iv) but you can distinguish them from (i), (ii) and (v). (i) Hexane: 3 13C δ shifts (ii) 2-methylpentane: 5 13C δ shifts (iii) 3-methylpentane: 4 13C δ shifts (iv) 2,2-dimethylbutane: 4 13C δ shifts (v) 2,3-dimethylbutane: 2 13C δ shifts
13C NMR spectra above.

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The chemistry of ALKANES revision notes INDEX

The infrared spectrum of hexane

The H-1 NMR spectrum of hexane

The C-13 NMR spectrum of hexane

Mass spectroscopy index

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